View Full Version : Metagenomics
- PubMed: Profiling model T cell metagenomes with short reads.
- public database for metagenomic sequences
- Antarctica metagenomics research
- PubMed: Comparative day/night metatranscriptomic analysis of microbial communities in
- PubMed: Metagenomic analyses of viruses in the stool of children with acute flaccid p
- PubMed: Analyzing Gene Expression from Marine Microbial Communities using Environment
- PubMed: Methods for comparative metagenomics
- PubMed: Metagenomic signatures of 86 microbial and viral metagenomes.
- function/abundance prediction from reads
- PubMed: Suppression Subtractive Hybridisation for Metagenomic Subsampling
- TerraGenome Consortium
- NIH Awards $42 Million to Human Microbiome Projects
- PubMed: Exploring the oral bacterial flora: current status and future directions.
- PubMed: Microbial community structure in the North Pacific ocean.
- step by step for rarefaction calculation
- Rarefaction distance explanation
- Assembly of short reads in Metagenomic studies
- filtering samples
- Mapping against multiple sequences
- Illumina Metagenomics data
- Meta assembly
- 454 metagenmic data assembly
- Rapid Identification of Microorganisms in Solexa samples
- % identity cutoff
- Sample/library prep of DNA and RNA in a metagenomic sample
- Tools for Phylogenetic Trees
- Comparing shotgun metagenomic reads: 454 vs HiSeq
- metagenomics pcr in triplicate-why?
- Normalization of 16S PCR products
- sanger end-seuqencing of metagenomic fosmid library
- Meta-Velvet
- k-range in Meta-IDBA
- best 16s region to amplify with NGS ?
- the review of metagenomics assembly
- Publicly available Illumina metagenomes
- MIRA assembler for metagenomics
- SOlid &&&& Metagenomics
- MetaCV: a composition-based algorithm to classify metagenomic reads and function
- 16S metagenomics, how much data needed?
- Metagenomics analysis with CLOTU: problems with input data
- 454 vs MiSeq - Need to optimize time/cost for 16s analysis of 300 Stool Samples/month
- Tool to identify 16s rRNA fragments in raw data
- Quantitative 16S profiling with multiple 16S genes per genome
- How deep to sequence?
- how to deal with 16S rDNA data form Illumina
- analyze 16S metagenomic 200bp data to species level
- 16S rDNA sequencing
- Who uses a MiSeq for 16S data?
- Removing Chimeric sequences from Metagenomics samples
- Species abundance and rarefaction in metagenomics data
- Pulling bacterial and fungal seq apart
- Help/advise to NGS virgin....
- V4 region primers
- Metagenome assembly
- Assemblers
- Examination of PCR biases in 16S experiments.
- Mg-rast --> megan
- QIIME constraints and time to run for 16S Illumina
- Differential gene expression on metatranscriptome data
- survery: what assembler, gene prediction and gene annotation softwares do you use?
- 18S profiling primers
- fungal ITS profiling primers and 500bp Ion Torrent amplicon sequencing
- Sequencing 400bp 16s Amplicons on the PGM
- Sample collection for metranscriptomic sequencing
- Taxonomic assignment discrepancies between SILVA and GenBank databases
- Denoising Illumina reads
- Fungal ITS amplicon sequencing (NexteraXT vs TruSeq Custom Amplicon)
- Silva database
- Sequencing for enzyme discovery - Miseq or 454?
- Tophat for metagenomes?
- Depth & Length for individual genome reconstructrion
- chimera - uchime
- Megan for contig or gene classification
- metagenomics databases and summary
- Advies on tool selection
- MG-RAST - remove or retain non-overlapping paired-end reads
- 454 16S data from QIIME - what next?
- Polymerase of choice for generating 16S amplicons?
- Genome extraction from metagenomes
- demultiplexing data
- mothur extract the .flow data from sff file
- how to make a matrix of OTU abundance in each sample
- Organism promoting for Drought Resistant
- Metagenomics/Metatrancriptomics Sequencing
- assemble conitgs in metagenomics
- HUMAnN for non-HMP?
- Best way to search for gene homologue in metagenomic dataset
- Not sure which questions to be asking, or how to answer them (metagenome, metabolism)
- Best approach to analyze taxonomic profiling of metagenomes from environmental sample
- Using MetaVelvet, what hardware requirements?
- Bacterial species definition / OTUs
- Which software could be suitable for different cutoff value?
- How to use QIIME process MiSeq 16s data?
- Metamos help request
- Hai, I need clear protocol for DNA Barcoding in bacteria
- How to install qiime?
- MetaVelvet not running
- Can I combine 16S and 18S rRNA in one sequencing run?
- how to get gene abundance
- simulate metagenomic reads
- How do I assemble long and short contigs togeather?
- COG database
- the weighted UniFrac distances are bigger than one is normal ?
- Metatranscriptomics and residual human sequences
- Does anyone have a recommendations for graduate-level course on metagenomics?
- Best platform for metagenomics?
- Illumina 16S libs - tech & QC questions about construction and data comparison
- Species level identification in oral microbiome samples?
- Best classifier for viral reads--PhyloSift? BLAST? Others?
- OTU picking
- BLAST comparison of 16S rRNA against the SILVA database
- Fungal ITS sequencing Illumina
- Scaffolding or not?
- Downloading metagenomes from ncbi from terminal
- Considerations for a pilot study: HiSeq SR100 vs. MiSeq PE300
- Best 16S region for 300PE Miseq
- Need help to prepare sample for pyrosequencing
- App 16S metagenomics basespace illumina- rarefaction curves
- reps and analysis
- NORMALIZED tetranucleotides frequency
- Tool for viral metagenome assembly with extremely low coverage?
- Resequencing the same Illumina library several times
- Functional annotation
- Visualizing number of hits on KEGG map
- Amount of data for metagenomic analysis
- How to visualize microbiome datasets ?
- MiSeq v2 cartridges for metagenomics
- Minimum quantity of DNA per sample to pool?
- ngs tools and database
- Theoretical Distribution_GC Distribution_FastQC_Metagenomic Data
- 16S gene genomic coordinates?
- Free alternative to KEGG
- Comparing metagenomes produces with different sequencing technologies
- Bad assembly or bad sequence data?
- filtering out human contaminants
- seek help about UniFrac.zip
- Comparing OTUs from different V regions?
- MEGAN and blast against NR
- Illumina bacterial metagenomics
- MiSeq Reporter Metagenomics Workflow
- Illumina MiSeq 16S run quality
- Is dereplication necessary?
- Mismatch between PE reads
- beta diversity depth
- Understanding 16s RNA reads
- Recommended output or reads for 16s metagenomic
- high number of denovo OTU
- shotgun metagenomic sequencing coverage
- Pathogen and Probiotics database of 16S rRNA
- How much data should I generate for metagenomics/metatranscriptomics?
- Two band/peak corresponding to 400bp for V4 region
- Human contaminants in viral metagenome
- Hello All.I have annotated my metagenomic dataset using MG-RAST and now want to gener
- Redundancy analysis (RDA) heatmap for 16s NGS results
- Data I can't understand
- 1st metagenomic experiment
- Metagenomics, How much Ntd data is generated per sample in different NGS platforms.
- Extracting and scaffolding microbial genomes from complex communities
- Making a in silico mock community
- Many homopolymeric reads
- Associate gene names to respective abbreviations
- Paired-read analysis in MEGAN
- How To Run 'Merge' in the Wonderful New checkM Package
- What's the best way to identify the taxonomy of assembled genomes?
- Viral metagenomics sample with a high concentration of bacteria
- Controls to Consider for Metagenomics Project
- Experimental design
- Scaffolding tools for metagenomics ???
- MG-RAST - Alignment parameters of their process statistics?
- Megan attibutes file format
- modify megan5 taxonomy paths output
- Assigning taxonomy to shotgun metagenomic reads: sequence alignment or composition?
- MEGAN: impact of max number of hits in read annotation
- Using CLARK and EBI for metagenomes
- 16S vs shotgun
- Graphic Tools for Taxonomic Assignments
- shell script for concatenating fastq files
- sequencing QC and metagenomics
- Microbial DNA extraction
- Resolve species/strain in metagenomic bin
- Using prokka in metAmos
- Clustering/Binning Metagenomic contigs with MyCC and 16S sequences
- auto log-off on IMG website
- Question about whole genome metagenomics for the microbiome?
- paired end data not aligned in NextSeq 500
- Extraction
- Culturable microbiome NGS
- New metagenomics analysis platform: Nephele
- Post binning
- MiSeq Micro/Nano Kits v2 for 16S?
- 16S triplicates
- Spiked-in control for microbiome
- Metagenomic DNA/RNA from human tissue samples
- EBI Metagenomics: How to analyze NCBI data?
- Training in Metagenomics Data Analysis @NIH, USA, Nov 7-10,2016
- Multithread MyCC
- inconsistency in aligning metagenomic data in Bowtie2
- 21,000 Human Microbiome Dataset Collection
- Concentrations of Post-indexed libraries
- Minimum amount of data needed for reliable results?
- MetaSUB Inter-City Challenge - CAMDA@ISMB/ECCB
- megahit failing without an error message in (x)ubuntu virtual machine
- Metagenomic survey of gut microbiota - depth, tradeoff and num. of samples to include
- Advice on assembling very large metagenomic dataset?
- How to extract subregions from Miseq 16srRNA data?
- Read lenght in 16S RNA data
- how to count the mapped reads with bbmap?
- Extraction of genomic DNA from RNAlater preserved cattle tissue Using DNA extraction
- What is the best DNA extraction kits for RNAlater preserved cattle tissue
- Convert mothur classify.seqs output to BIOM format
- Studying soil microbial communities
- Same sample different results
- Find single copy gene for bacteria and archaea
- QIIME vs Mothur vs UPARSE
- 16S sequencing tissue - host DNA contamination
- Processing a very large soil dataset
- Workshop: Metagenomics Analysis with MEGAN6
- raw illumina reads or assembled contigs for Taxonomy
- Illumina 16s protocol: size
- recA database?
- Best tool to find gene variants in metagenome data
- Normalization for NGS count data with high variance between observations / uneven com
- calculate genome bins' similarity
- quality filtering error usearch
- merge contigs of different K-mers of metagenomic data
- Alpha and betadiversity why??
- Generate local blast database with RefSeq bacteria AND taxonomy
- MetaSUB Forensics Challenge @CAMDA ISMB Chicago
- Crowdsourcing the Advancement of Microbiome Research: Mosaic & precisionFDA Challenge
- V4-V5 Region Using 2x250 - Enough Overlap?
- Simple statistics help
- I had a Metagenomic 16s rRNA run on MiSeq v3 kit 2 x300 cycles. with good PF >89% but
- Sanger Sequencing for Community Analysis
- FastQC results for 16s reads
- Statistical analysis of Centrifuge output
- Statistics for metegenomics analysisi form 3 archeologis sites
- how to represent my ngs results
- AAAAAA.. TTTTTTT.. heterodimers
- Centrifuge output question
- Shotgun metagenomic method to detect all organisms (quantitatively)?
- The Metagenomic Forensics Challenge - CAMDA19@ISMB/ECCB
- Metagenomics MG-RAST
- summary statistics of metagenomics
- Beginner in metagenomics
- Taxonomy tree conflicts in Greengenes V 13.5
- Taxonomy tree conflicts in Greengenes V 13.5
- GC content bias in ATCC mock reads
- How to distinguish between 16S chloroplast reads and real ones?
- How to use ARB nifH database(Zehr et. al) for taxonomic assignment
- SURPI database
vBulletin® v3.8.9, Copyright ©2000-2021, vBulletin Solutions, Inc.